Tips for Submitting a Thesis, A Retrospective: After the First Draft

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Phew! You’ve done it! You’ve just finished writing your first draft and sent it to all your supervisors. Now what? I was actually really surprised by just how long it took me between finishing my first draft, and submitting it to the examiners.

1)   Keep feedback expectations realistic

After several years of working together with your supervisors, most graduate students have a good idea about each of their supervisor’s styles. Some supervisors can issue vague instructions, others give advice down to the smallest detail, and still others will never give any advice at all. Feedback will come in all forms (see my post on February 22) but try and work with what you’re given. Generally, your supervisor will want to help you produce the best thesis possible, because your performance reflects back on them.

When sending the supervisors draft material, set deadlines for when you want to review it with them. Just as in my last post I recommended setting deadlines for your writing with your supervisors, the same is now reversed for setting deadlines for your supervisors feedback during a meeting with you. Make sure the deadlines you give them are reasonable, but do set a meeting time and turn up, regardless of how much you hear back from them in the meantime. If they repeatedly miss deadlines, assess the situation, and either apply more pressure or look for feedback from a different source.

2)   Keep turnaround time minimal

Your supervisors are going out of their way to make sure that not only did your experiments go well, but that your entire PhD does, including the thesis. An elegant PhD project with good results is only as good as the thesis your examiner reads. Because your supervisor is taking their time out to help with the thesis, it is important that they never have to edit the same thing twice. This is particularly true if you have several supervisors reading your thesis at the same time. It’s only fair to them, that you are not wasting their time, by having them correct something you’ve already corrected based on feedback from a different supervisor. Incorporate their changes, and distribute the latest draft as soon as possible. Obviously, rename the file so they know it’s a new draft.

3)   The Tedious Details: A Checklist

• Check the margin requirements set by the university.
• Check the line spacing.
• Check the word count.
• Check the font and formatting (particularly important for Microsoft in order to generate an automatic Table of Contents).
• Set the thesis language and use spell-check. As a scientist I confess that I often ignore the Microsoft spell-check, because a lot of the time it doesn’t know scientific terms. Go through and use it anyway, because it will catch common words that you’ve misspelled. And teach it the scientific terms (“add to dictionary”) – but make sure that you teach it the correct way to spell the word, otherwise it will forevermore be misspelled in your thesis.
• Check your spacing. I spent 4 hours one very tedious afternoon going through all 200 pages of my thesis and checking there were two spaces between all the sentences.
• Clarify any sentence that starts with the word “this”.
• Find synonyms for every time you’ve used the word “important” – your thesis is not that important.
• Find synonyms for, or simply remove all references to something “interesting” – your thesis is not that interesting.
• Take a deep breath and count to ten.

4)   Take care of the paperwork

Several weeks in advance of when you think you’re going to submit, check the paperwork requirements set by the University. You might find, as I found at Oxford, that some paperwork is due to be submitted 6 weeks prior to submitting the thesis and that this can delay the process if you haven’t submitted it with enough time. Also, check any paperwork that needs to be submitted at the same time as the thesis. Also, check for any further impediments to your thesis being accepted (as per my post on April 4th), and remove any obstacles.

5)   Assess the printing, binding, and submitting situation

One of my flat-mates who recently submitted her thesis warned me that the process on the day of submission takes longer than you might think it should. That is certainly true. One of the things to decide is where to print the thesis. Crucially for this is the decision of how many, if any, pages should be in color and also the cost of printing vs. photocopying. Then, figure out how the thesis is going to get bound (again, check the university regulations), and if using a company to professionally bind the thesis, find out their opening hours. Most importantly, figure out the opening hours of the university office that is going to be accepting the bound thesis. Buy any envelopes etc. needed.

6)   The final day

If you have not yet done so, reread the entirety of the thesis to check for any last-minute corrections. Make sure to do this while fully awake. Update the bibliography. Update the table of contents. Convert the document to a PDF. Print using the PDF. Partway through the printing, check the printed pages to ensure that your printer has not run out of ink. I printed about 50 pages that had to be reprinted from a different printer because the printer had run out of ink and the quality was unacceptable. Hand the thesis to the binder then wander around the city in purgatory until you can return to pick up your finished product. Take the thesis, with any necessary paperwork, to the appropriate university office and submit it.

7)   Book a holiday

At some point during the time between writing the first draft and submitting the thesis, book a holiday to start a few days after you’ve submitted. By then you’ll have recovered from both the exhaustion of the last few days, and from the partying after submitting. Go somewhere different and relax. If you’re lucky, get engaged.

Tips for Submitting a Thesis, A Retrospective: Getting to the First Draft

Previously in my posts I’ve outlined my feelings on the general structure of writing a science thesis, and what the style and substance of each section should be. In this set of posts I’ll discuss my retrospective advice on the easiest way of writing a thesis.

1)   Write a Literature Review your first year

Quite a large portion of my literature review/introduction section of my thesis was written in the first year of my PhD. In my second year this was easily cut, pasted, reformatted, tweaked, and with the addition of a few paragraphs made up the introduction section to my transfer report (standard mid-way thesis in England).

In the third and fourth years, I updated the original literature review to include the latest papers and to incorporate changes in the experiments that had since been made. For example, genetically modifying cells to overexpress growth factors had originally been planned, but later changed to simply adding growth factors to the system. This meant that while the overall gene transformation section was scrapped, the section on each individual growth factor could still be used.

This preparation throughout the course of the PhD not only means that less writing needs to be done at the end, but also gives context on where your experiments stand in the context of the research community. This can both give you ideas for new experiments and also lead to the abandonment of experiments, which have been shown to be futile (though usually the former).

2) Set aside time at the end of the PhD to write and not do any experiments

Having time to focus on organizing the thesis and simply writing, without simultaneously carrying out experiments is a luxury. Some supervisors will allow you to do this, and others will not. Try and set a deadline when experiments will stop and stick to it. I was lucky in that I had a plane ticket to leave the country, and go into a different environment, but I know many students who either feel pressure from supervisors to concurrently work on experiments, or who, of their own volition, keep striving to get “just one more” piece of data to put into their thesis.

Continuing to carry out experiments leads to two main problems. The first is that research takes up time and focus. This necessarily draws time and focus away from writing and disrupts writing momentum. I made all the results figures for my thesis within 5 days. On a separate hot streak, I sat down and wrote the wording for the results section in about 3 days. That simply cannot be done if you’re spending hours out of every day working in the lab. Even when you sit down to write, either anxiety about the potential outcomes of those experiments, or plans for the next day’s work are going to be running through your head.

The second main problem with continuing to work on experiments when writing up, is that it detracts from the solidity of the thesis itself. If one is constantly trying to figure out where the current experiment is going to fit into the thesis, or even worse, where future experiments are going to fit into the thesis, then the format of the thesis never solidifies. It is much more difficult to write when the contents are not set. Particularly when working on a piece of literature, such as a PhD thesis, where all the components need to fit together, it’s important to be able to step back and see the larger picture; difficult when experiments, and sometimes whole sections may be missing.

3) Set deadlines and find people to hold you to them

It’s often easy to set a deadline and then watch it slip past. It’s harder to set a deadline and watch it slip past, if that deadline involves a meeting with your supervisors to go over a specific goal you had set to accomplish by that deadline. If you disagree with that statement, find someone who’s not as nice as your supervisor, someone you care about not disappointing, and set a deadline with him.

When I moved back to Oxford, my lab offered to set me up with a desk in the office where I could write. I decided against having any space in the lab, because I wasn’t doing any experiments, because the lab is outside of the city center and would involve a long commute, and because I felt like I needed a different writing environment (see Tip 4). This meant that the only time I came into the department was every 2-3 weeks, on a date I’d set with my supervisors at the previous meeting, to discuss my progress.

If you’re working in an office, and people see you sitting at your desk 9-5, then they automatically assume that you’re being productive during that time. If however, you’re working out of the office for 2-3 weeks without anyone seeing you, then the pressure is on you to turn up with product at the end of that time. Otherwise, they’ll assume you were sitting around in your pajamas all day catching up on BBC television shows.

Find someone, set a goal, and a date to review your progress on that goal. Turn up for the meeting on that date, having met your goal, and receive their approval. Repeat.

4) Find an environment that stimulates your writing

I do not write well in my dorm room. I procrastinate very well in my dorm room. I will tidy. I will wash the dishes. I will cook. I will surf the web. I will reorganize my entire closet and take pictures of each item to organize my wardrobe using an app on my iPad (yes, I did do that).

When I lived in DC I had to figure out the environment I needed for the literature review. I found that if I was trying to read a lot of papers in one day, that I would get easily distracted, no matter where I was, if I could check my email, etc. on the internet. I figured out that what worked very well for me was going somewhere without internet, with a stack of printed papers, and a highlighter, and even with my computer to write notes on, but somewhere without internet access. The Smithsonian Institutions museums worked very well for this – particularly the National Gallery and the National Portrait Museum. Both even have a café where you can get lunch and coffee, but no Internet access.

When I started writing in Oxford, I first tried to work in the Radcliffe Camera, one of the library buildings at the university. It’s an absolutely gorgeous building, and full of studious scholars, but I quickly found that the atmosphere was too stifling. I ended up writing the vast majority of my thesis in the café at Blackwells Bookshop on Broad Street in Oxford. This café offered me the four things I found necessary to stimulate my writing: free wi-fi, plug sockets for my computer (so that I wasn’t limited by battery life), coffee, and ambient noise. I’ve found that I actually find background noise comforting, and surprisingly less distracting than silence. In the library I felt pressured to work, in the café I feel relaxed and able to work. And the coffee doesn’t hurt either – after all, it’s buy 10 get 1 free!

Image from http://www.phdcomics.com

How would you like your feedback today?

I have 6 supervisors. So far, I have received draft edits from 3 of them:

• Supervisor 1: read the thesis Intro, then reread the whole thing at a later draft version
• Supervisor 2: has read everything but the conclusion, but can’t seem to stomach reading 5 more pages
• Supervisor 3: has read the whole thing through, and reread the entire second half
• Supervisor 4: read 2 pages
• Supervisors 5 and 6 have not read anything as far as I know

And my mother was the first person to proofread the entire thesis.

So far I have edits in a variety of media:

• Supervisor 1: prints out the drafts, writes on them with red pen, and gives them to his secretary, from whom I pick them up
• Supervisor 2: has sent me “track changes” documents
• Supervisor 3: prints out the drafts, marks them up, scans them, and puts PDFs in a shared folder

And my mother sent me track changes.

So far the comment highlights have included:

• “I’m sorry, it’s really difficult when experiments don’t work out. (my mother)”
• “This looks weird.”
• “This is almost boring.”
• “Surely you didn’t perfuse the whole mouse?!”
• And “too verbose”.

I’m currently on draft #6. I haven’t yet labeled any documents as “final” yet, but I do have several “final figures” folders. I love  this comic by PhDComics, but it doesn’t quite show the enormity of having two different computers open, one with edited documents, and one with the original document, constantly scrolling through and tweaking the thesis.

 

Thesis Writing: The Middle Chapters

The middle chapters of the thesis include the Methods, Results, and Discussion sections. These are, to a certain extent, the hardest chapters of the thesis to write. Unlike, for example, the introduction, it’s not simply a questions of laying out your ideas, looking up what other people have done that is relevant, and discussing their work. The Methods section, I grant you, is very straightforward as long as you have documented what you have done along the way – you, after all, should know what experiments you did. The Results section is slightly trickier, in that you need to figure out how to logically and best present your findings in a way that conclusively demonstrates your point without overwhelming the examiners with extraneous data or confusing them. The Discussion section is by far the most difficult as you must evaluate your data and explain how it fits in with the overall aims of the project.

So far, in my posts on thesis writing, I’ve discussed the general format of the thesis (August 27) and my current efforts with the results section (November 17). Particularly, in the August 27^th post, I stressed that the PhD is not simply a long paper. That said, there are countries in the world, e.g. Sweden, Finland, the Netherlands, and Australia (to name a few) that will accept several papers written by the student (and published in peer-reviewed journals) stapled together in lieu of an actual thesis.   If thesis writing were like just writing a long paper, there would be the following sections: Introduction, Materials and Methods, Results, Discussion, and Conclusions. However, many people would argue that while a thesis needs an Introduction section as well as a Conclusions and Future Work section, the middle chapters should not be so strictly organized. Rather, the belief of having several middle chapters based on various themes or questions pertaining  to the overall project which each contain subsections of Materials, Results, and Discussion, is becoming increasingly prevalent within the scientific academic community.   In fact, a friend of mine who recently defended in Oxford had organized his thesis as if a long paper and was told that for his final version the only alterations desired were that he cut and paste his sections in the latter method to tell a better story.

Part of the reason why this approach of having self-contained chapters that each contains several parts, is that it lends a better flow to the thesis. Because theses tend to be so long, it becomes difficult for an examiner (one dare not hope that anyone other than the examiner will actually attempt to read the full document) to read each section in its entirety and keep it fresh in their mind as they go on to the next section.  Indeed, if organized thusly, the method, results, and discussion of a particular method could be spaced out with 20 or more pages in between them – hardly allowing for the formation of a sense of direction. However, by splitting the middle section of the thesis into topical chapters, this allows for the examiner to focus on a smaller topic at each time, with a sense of how each experiment was performed, what the results are, and how to interpret these results in relation to other experiments which also answered the same question. Then, with an idea of how each topic was addressed, the parts can be brought together in the final Conclusion section to show the larger picture.

The simplest way, perhaps, of explaining this concept is to think of the difference between a nursery, and a garden.  If the Methods, Results, and Discussion sections were three types of flowers, then the more traditional method would be akin to a nursery; each section would be taken care of, but separately and in neat little rows. However, the newer method would see that although a garden contains these three types of flowers, in contains them in several beds which contain clusters of each type, so that the flowers can be seen in relation to each other, followed by the design and layout of the beds.

Oxford – Bring on the Thesis

I’ve been back in Oxford for two weeks now.  Finally got over my jet lag. Maybe I shouldn’t have slept during the daytime the entire flight over from the States. But it took me longer than usual to get over the jetlag – in part due to a newfound love of afternoon coffee and partly due to what is possibly the best duvet in the world.

 

So how’s the thesis writing going, you ask? Well, I must say that the Radcliffe Camera in Oxford is an amazing place to work. Opened in 1749, it’s a place full of history, and the sound of students working. There are also many coffee places I go to when in need for more ambient noise, and caffeine.

 

But the writing, I hear you ask, how is the writing going? Well, the first thing to do is to figure out the data that you have. To this end I need to finish analyzing some data, which is what I’m currently focusing on. Also, for the writing part, I’m working on the words that go in the results section. The Results section is always trickier than it might appear because all the figures and relevant graphs need to appear there in order to present the data, but in terms of prose it’s important to provide context for the figures, while at the same time not including that which should instead belong in either the Methods or Discussion sections.  Often, so far, I’ve found myself writing and then thinking that a paragraph really belongs in another location in the thesis.

 

So here are the steps now:

1)     Finish analyzing data

2)     Write Results section

3)     Make figures and insert into Results section

4)     Reformat Methods and Intro to fit around the Results section

Autumn: Status Check

So here it is, the end of summer. The beginning of Autumn. I’m leaving the NIH and moving back to Oxford November 1. This is a rather arbitrary date, but then again, as I’ve come to learn, many things in the life of a PhD student are arbitrary. For a long time the date was October 1st, but then a shipment of mice back in May was backordered by several weeks, so it got moved back a month.

November 1. 39 days.

So far, everything seems to be reasonably under control. I learnt how to do qPCR last week so there will be a lot qPCR stuff. And the last big surgery was done on Thursday of last week, with the DIVAA transplants coming out in 2 days. Oh, and my final regular transplants were embedded yesterday and will be sectioned tomorrow. Finally, everything seems to be coming together.

Except for the staining. In order for my grand PhD scheme to work I need to stain and quantify the amount of blood vessels in transplants. So far, I haven’t yet gotten this to work, and it’s imperative that it starts to work soon. Because I intend to retroactively stain all the slides I’ve made during my. This quantity to get through is really large, and will take time to stain, image, quantify, and analyze. The staining is the one huge hurdle to my success. I may have to take some of it to Oxford to finish there, which goes against my plan of just writing and not doing any bench work in Oxford – but hopefully I can finish before then.

So… I’ll keep updating the blog regularly – the next blog post is going to be about how to measure the velocity of cells. Please also check on me on Twitter (@makingbones) – starting October 1st I’ll be tweeting daily on progress in the countdown towards the big move!

Thesis Writing: Backing Up

Every PhD student, towards the end of her research, becomes just a tad (or very) paranoid that they’re going to lose all their research. Back in the day before computers, students had lab notebooks with all their results and doodlings, along with photocopies of relevant papers. If you go not too far back (only about 30 years ago!), we reach the realm of typewriters, and professional medical media artists. These days the student has word documents with all their plans and proposals, powerpoints from seminars and poster presentations, and countless PDF files of scientific papers. The medium may be different, but the concern is still the same.

What happens if I lose all my research?

What if the building catches on fire and my papers burn up?
What if the professional typewriter loses my copy?
What if my computer crashes?
What if someone deletes my files from the shared computer?

So what’s the solution? The solution is to back up.

We are often told that. But what does backing up mean?

I used to transfer my files between computers on an external hard drive. This meant I had all my files on both my work and home computer and the external hard drive. This worked until instead of working on the actual computer and then transferring files between computers I decided it was easier to just keep the most recent copy on the external. Soon I was only using the external and my computer files were a few months out of date. Then, one day, the external got knocked off a table and broke when it hit the floor. The files had to be restored by a technology company for $1600. This, obviously, was not what was meant by “backing up”.

After the incident when my lab paid $1600 to get a few months of data back, I started using “the cloud”. I started using Dropbox, because I realized I needed a way of syncing my files between computers, without relying on an external or USB. The bonus with Dropbox is that the synced files are also stored on the hard drive of computers with the program. This means I have the most up to date files on 2 different computers, should the online system go down for whatever reason. Additionally, I back up once a month to a “shock-proof” external hard drive; perfect, giving the precedent I set. The cloud is amazing. I can work on my files from multiple computers without the need to carry stacks of papers (the old-fashioned way) around with me, or even just a USB stick (the less-old-fashioned way).

I do have one special backup method for my thesis write-up. A USB necklace. If the internet dies, my hard-drive gets smashed by a bulldozer, and both of my computers go up in flames, I’ll still have my thesis around my neck.

That’s my thesis insurance.

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Thesis Writing: Is a Thesis Just a Long Paper?

University of Oxford Notes of Guidance: Preparation and Submission of a Thesis

These notes of guidelines offer very little in way of succor to the poor graduate student trying to tackle the daunting task of writing a thesis. A scientific thesis can be construed as an extremely long scientific paper with the same components, however there are many important distinctions.

• I vs. We: Peer-reviewed publications use the royal “we” to infer all the authors on the paper (with the general knowledge that some people contributed more than others depending on their placement in the author list). Thesis writers use the term I and take personal credit for all the work that they have actually done. Of course, due credit is given to work previously carried out by the lab or done in collaboration with other researchers.
• “As described previously”: A term often used in peer-reviewed journals and accompanied by a reference to either a previous paper from the same group or a different group they stole the method from. This chain of “as described previously” especially accompanied by the term “with a few minor alterations” can go back multiple papers to the point where the technique that one is actually looking at can’t be determined by tracing it back. In a thesis the entire procedure is detailed in nauseating depth. This is incredibly important because a thesis is supposed to be reproducible, even more so than a peer-reviewed publication. Additionally, the specificity of protocols allows the protégé of the student, and there often is one in academic labs, to easily grasp what was done.
• Literature section: Literature sections in peer-reviewed papers are often called background, and are meant to bring the reader into the specific content within a few short paragraphs. In a thesis the literature review starts out much wider in scope and waxes lyrical for many pages, citing many references (more like a review and less like an article), discussing all components in the wider scheme and then bringing them together to discuss the niche topic.

So far I’ve made a draft each of the Methods and Literature Review sections. This week’s task is to tackle the results section, bringing all the different graphs together and organizing the figures.

 

Wish me luck!

Thesis Writing: Psychology of a Thesis

How does one begin to write a thesis? More importantly, perhaps, how does one keep up the strength to write the entire thesis through to its bitter/sweet end? These questions loom over all graduate students from Day 1 of their course. Some days the worry stands out more, on other days it’s possible to get distracted by actually doing the research and forget that one day it all needs to get written up. Some days one thinks about the writing process and tackles some small aspect of it, on other days the worry is there but we push the worry deep within us, very much like the proverbial ostrich with its head in the sand. There is, however, no denying that thesis writing causes grad students much stress. This was demonstrated by Izawa et al. in 2003, who wrote a paper showing elevated stress marker levels in students just prior to thesis submission.

Episodic stress associated with writing a graduation thesis and free cortisol secretion after awakening

There is an abundance of advice on the web for students about to embark on a thesis project. This includes advice to students by universities, such as these pages from Dartmouth and Yale:

Dartmouth: Writing a Thesis

Yale: Writing a Thesis

And, touchingly, there is this advice from the University of Oxford to advisors of students writing theses:

Oxford Learning Institute: Writing a Thesis

Then, depressingly, there are many companies that make money off students who use their services, because they don’t have mentors who have told them not to. Companies, such as one site I saw while researching for this blog post (but won’t deign to put a link to here), even claim that they can specifically help you write your Oxford thesis (with poor grammar, going by the standard of their website). But, more importantly, such companies not only take advantage of students who are psychologically vulnerable, they also damage the integrity of those students.
On a brighter note, there is a light at the end of the tunnel! Even though graduate students slave away at writing and research, one day that writing and research is all complete. Then, we stand at the exit from our cave, gazing out into the real world (hopefully with degree in hand). Some yearn to return to the days of flexible hours: sleeping in some days and pulling all-nighters and sleeping in the lab on other days. Some yearn to return to our graduate student stipends: not that the money was all that great, but rather that we could be paid to be students (who knew?!). But the important part is that eventually, despite our raised cortisol levels, most graduate students do finish….

Well… about 55-65% of them finish, as shown by the PhD Completion Project:

Council of Graduate Schools: Ph.D. Completion and Attrition